The Snowden leaks gave a pretty good picture of what the capabilities are. They do most certainly not have backdoors into every possible crypto system.
SHA1 should probably be replaced for example, but thats not all crypto by a longshot.
Their are good talks at the C3 confernce about 'Post Snowden Crypto', specially by 'ruedi'. He goes into detail about all the major crypto system and explains how risky they are, and what we know about the NSAs efforts to break them.